dme-mir-4940- Best orthologs

dme-mir-4940	chr3L:9137692-9137797 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 9137715-9137736
   star strand at position 9137754-9137775
   mutations
   read mismatches

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3L:9137677-9137812 +		1	CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------TATCGCAACTTATC----GATCGGGTGGCGGATAT----------AGATCAT-----------------T---------G------------GTTA----TCCC-TT---A-------------------------------------------------------------------AT--------T-----AAA----GC--------AAACAAG------ATTTGTTTCGGCCGC---CCGATT-T---------------TACATACAACGACACGAATA----------------------------G---CAGGATATAG
droSim1	chr3L:8545595-8545743 +	LASTZ	4	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------TATCGCAGCTTATC----GATCGGGTGGCGGATAT----------AGATCATAGCAAGCCCTATCGAATT---------G------------GTTA----TACC-TATTAA-----A------------------------------------------------------------------------------------GC--------AA-CTAG------GTTTGTTTCGGCCGC---CCGATT-T---------------TACATACAACGACACAATAG--------------------------------CAGGATATAG
droSec1	super_0:1396669-1396817 +	LASTZ	4	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------TATCGCAGCTTATC----GATCGGGTGGCGGATAT----------AGATCATAGCAACCCCTATCGAATC---------G------------GTTA----TACC-TATTAA-----T------------------------------------------------------------------------------------GC--------AA-CTAG------GTTTGTTTCGGCCGC---CCGATT-T---------------AACATACAACGACACAATAG--------------------------------CAGGATATAG
droYak2	chr3L:2783249-2783373 -	LASTZ	0	CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTCGC----GATCGGGTGGCGGCTGT----------AGATTGT-------------------------------------------------CCT-TG---T-------------------------------------------------------------------AT--------C-----AAA----GG--------AAAAGAG------ATTTCTTTTGGCCAC---CCGATT-C---------------AAAATACAACGACACAATAG--------------------------------CAGGATATAG
droEre2	scaffold_4784:4908876-4909031 -	LASTZ	0	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTATC----GATCGGGTGGCGGATATACCCGTGCACAGATTGTAGCACACCCTATCGAATT---------G------------GAAT----TCCC-CATTAA----AA------------------------------------------------------------------------------------CT--------GA-GTGG------GCTTATATCGGCCGC---CCGATT-C----------------ACATACAACGACACAATAG--------------------------------CAGGATATAG
droEug1	scf7180000409467:339436-339588 +	LASTZ	0	CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTATC----GATCGGGTGGCGGAAAT----------AGATTGTAGGAAGTTTTACT-AATT---------G------------GACTTT--TCCC-TATATA-----A------------------------------------------------------------------------------------GT--------AA-ATAGAAAATAGTTTATTTTGGCTGC---CCGATT-T---------------AACATACAACGACACAATAG--------------------------------CAGGATATAG
droBia1	scf7180000300910:2070791-2070920 -	LASTZ	0	CCGG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT------------------ATC----GATCGGGTGGCGGAAAT----------AGATTGTAGCC----------ATTT---------G------------GATT----TCCC-C--A-TAGAGAA------------------------------------------------------------------------------------GT--------GA-AT-------AGTTTATTTTGGCTGC---CCGATTCT---------------CACATACAACGACACAATAG--------------------------------CAGGATATAG
droTak1	scf7180000415356:50643-50795 -	LASTZ	0	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GTCACTTATCGATCGATCGGGTGGCGGAAAT----------AGATTGTAGAAAGCTCTATT-AATT---------GAAAAT-----------CCAATCCC-CATATA-----A------------------------------------------------------------------------------------GT--------AA-AT-------AGTTTATTTTGGCTGC---CCGATT-C---------------CACATACAACGACACAATAG--------------------------------CAGGATATAG
droEle1	scf7180000491193:3377542-3377694 +	LASTZ	0	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACACAGACGGACA-------A---GCAACTTATC----GATCGGGTGGCGGCAAT----------AGATTGTAGTAAGCTCTGTT-AATT---------G------------GATATTG--CCCCT--ATA-----A------------------------------------------------------------------------------------GTACAT----AAA-TA--TGATAGTTTATTTTGGCTGC---CCGATT-T----------------TAATACAACGACACAATAG--------------------------------CAGAATATAG
droRho1	scf7180000777034:211800-211946 +	LASTZ	0	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTATC----GATCGGGTAGCGGAATT----------AGATTGTAGTAAGCTCTATT-GATT---------G------------GATATTG--TCG-C--ATA-----A------------------------------------------------------------------------------------GTACGT----AA-AT-------AGTTCATTTTGGCTGC---CCGATT-C----------------ACATACAACGACACAATAG--------------------------------CAGGATATAG
droFic1	scf7180000454065:2533611-2533748 -	LASTZ	0	CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCGGACGGACT-------G---GGAACTTATC----GATCTTATCG-----AT----------AACTTAT-----------------CGGTTAACT-TCGTTT-----------TCA--GCC-C--A-A-----A------------------------------------------------------------------------------------GT--------AAA-TA--TAGTAGTTTATTTTGGCTACCACCCGATT-C----------------ACATACAACGACACAATAG--------------------------------CAGGATATAG
droKik1	scf7180000302373:173620-173654 -	LASTZ	0	ATTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---------------AAAAAATATATAAGGCATAG--------------------------------TATGGTATAG
droAna3	scaffold_13337:19535893-19536018 +	LASTZ	0	CACT-----GCGATCTCGAGTACTTTGATCTC-------------------------------------------------------------------------------------------------------------------------------------------------TCTTCTC----A--GGGCCCCAAAAAGT----------ATGCTATGAAATATTTCGTT-TGCT---------A------------------------------------------------------------------------------------------------------------------AAG----TG--------TTTCAAG------GATTCTTTTGCGAGC---C----------------------------CACCTCAAGGATGT--------------------------------CAAACTCTAG
droBip1	scf7180000396360:730594-730829 +	LASTZ	0	AAAAACACTGCGATCTCGAGTACTTTGATCTCTCTTCTCAGGGCCCCAAAAAGTATGCTATGAAATGTTTCATTGCCAAAGTGTTTCAGAGGATCCTTTTGAGAGCCCAACTCACGGACGTCAAACTCTAGAGATGTCTCTTTTAAACCGACTCAGACGGACTTTGGTCT--TTGCAGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA--AGG----CAGATCAGGCAGG---ACTATA-T----------------ACATACAACGACACAATAGCAGGACTAT---------------------------CTATAG
dp4	chrXR_group5:393309-393508 -	LASTZ	0	C-AG--------------------------------------------------------------------------------------------------------------------------------------------------ACTTAGACGGACTTCAATCTA---GCAGTTTAAC----GATCGGGAAACGGGAAT----------AAACCAAAGTCGGC---------------------------------------------------------------------AGCCTATCCATCAAAATTCCAATATAATCACAACAGAAATCCAATTTGTTGC-----------------------------------T-------GGTTTATTTACGTTTC---TCGAGC-C----------------ACATACAACGACACAACAGCAGGTCTTCAGATAACTCATATGAAATAT---ACTTATGCGG
droPer1	super_9:3484001-3484112 -	LASTZ	0	GCAT--------------------------------------------------------------------------------------------------------------------------------------------------ACATAGGCATCGC-------A---TCCA------------TCGGG--------------------------------------------------------------------GTC----ACCC-G--G-TGGAGGA---------------------------------------------------TAAATTTTGCGG--TGGTAACCCCGCAACACAAGCACTC------------------------------------------A---------------CACACACAGCGACCCAAACA----------------------------C---GTGCAATAAC
droWil1	scaffold_181096:6035694-6035827 -	LASTZ	0	TCAG--------------------------------------------------------------------------------------------------------------------------------------------------GCCTAAAATTAGT-------TGCCATAACT-CTC----ATTTATATAGTAGATTT----------GATGCTTTTTTG-----------------------------------------------------------------TTTT----------------------------------------------------TT--------T-----AAT----AT--------AT-TAAA------ATTTTTATTA-ATGC--------------ATTTCAGTGTAAAAATTAAAATGACACATTTT----------------------------T---CCTTACGTAA
droVir3	scaffold_13246:101577-101715 -	LASTZ	0	CAGG-----------------------------------------------------------------------------------------------------------------------------------------------------CAGACGAAA--------------GTATCTCC----GACCCCATGAAGTGTAT----------ATATTCT-----------------TGATCAGCATCAATAGCTGAGTCGAT-------------GTA-----GCCATGTCCGTCT------------------------------------------------------------------------------------------------GCCTGTCCGTCCGT---CCGTCC-GTATGTA--------------TGAACGCAAGGATCT--------------------------------CAGAACCTTT
droMoj3	scaffold_6540:2381798-2381917 -	LASTZ	0	GTAG--------------------------------------------------------------------------------------------------------------------------------------------------ATTCAGTTGTACT-------TTATAGAA--TTTC----GATTTA------------------------------------------TGT----------TAAAAT-----------TCA--TCC-C--T-T-------------------------------------------------------------------AC--------C-----AAT----AT--------AT-ATG-------TGTTTTTTCAAATGC-ATGCATT--T---------------TAATGGTATCAACACAATTT----------------------------G---AAAGTCTCAT
droGri2	scaffold_15074:3698733-3698860 +	LASTZ	0	CTGA--------------------------------------------------------------------------------------------------------------------------------------------------ACATAACTGAATA-------A---ATT-----------------------------------------------------------------------------------------------------------------------------------------------------CACAACAT--ATTTAGTCAGTTACTTATGTATATACTTGATACAATTGTGCAAACATGCAAA------ATTCCAATTAAATGT--------------------------------------CACAATAT------------------ATAAAAACTGATGCGAGAAGATTG

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	CCAGACTCAGACGGACTTATCGCAACTTATCGATCGGGTGGCGGATATAGATCA-----------------TTGGTTATCCCTTAATTAAAGCAAACAAGATTTGTTTCGGCCGCCCGATTTTACATACAACGACACGAATAGCAGGATATAG
droSim1	CCTGACTCAGACGGACTTATCGCAGCTTATCGATCGGGTGGCGGATATAGATCATAGCAAGCCCTATCGAATTGGTTATACCT--ATTAAAGCA-ACTAGGTTTGTTTCGGCCGCCCGATTTTACATACAACGACAC-AATAGCAGGATATAG
droSec1	CCTGACTCAGACGGACTTATCGCAGCTTATCGATCGGGTGGCGGATATAGATCATAGCAACCCCTATCGAATCGGTTATACCT--ATTAATGCA-ACTAGGTTTGTTTCGGCCGCCCGATTTAACATACAACGACAC-AATAGCAGGATATAG

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

Small RNA-seq read pileup

Species

Alignment

droSim1

CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------TATCGCAGCTTATC----GATCGGGTGGCGGATAT----------AGATCATAGCAAGCCCTATCGAATT---------G------------GTTA----TACC-TATTAA-----A------------------------------------------------------------------------------------GC--------AA-CTAG------GTTTGTTTCGGCCGC---CCGATT-T---------------TACATACAACGACACAATAG--------------------------------CAGGATATAG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..............................................................................................................................................................................................................................................................................................................................................................................................A-CTAG------TTTTGTTTCGGCT..........................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
...................................................................................................................................................................................................TGGCGGATAT----------AGATCATAGCAAGC............................................................................................................................................................................................................................................................................	24	1	2.00	0.00	2.00	0.00	0.00
..............................................................................................................................................................GGACT-------TATCGCAGCTTATC----GATC.................................................................................................................................................................................................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................TGGCGGATAT----------AGATCATAGC................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................C--------AA-CTAG------GTTTGTTTCGGCCGC---C....................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................T--------AA-CTAG------TTTTGTTTCGGCC..........................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................................................................TAGCAAGCCCTATCGAATT---------G------------...........................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00

droSec1

CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------TATCGCAGCTTATC----GATCGGGTGGCGGATAT----------AGATCATAGCAACCCCTATCGAATC---------G------------GTTA----TACC-TATTAA-----T------------------------------------------------------------------------------------GC--------AA-CTAG------GTTTGTTTCGGCCGC---CCGATT-T---------------AACATACAACGACACAATAG--------------------------------CAGGATATAG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...................................................................................................................................................................................................................................CCCCTATCGAATC---------G------------GTTA----TACC-T.............................................................................................................................................................................................................................	23	1	1.00	0.00	0.00	1.00

droYak2

CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTCGC----GATCGGGTGGCGGCTGT----------AGATTGT-------------------------------------------------CCT-TG---T-------------------------------------------------------------------AT--------C-----AAA----GG--------AAAAGAG------ATTTCTTTTGGCCAC---CCGATT-C---------------AAAATACAACGACACAATAG--------------------------------CAGGATATAG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................................................................................................................................................................CTCGC----GATCGGGTGGT..........................................................................................................................................................................................................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................CTACxC----GATCGGGTGGC..........................................................................................................................................................................................................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................CAGACGGACT-------A---GCAACTTCGC----GATC.................................................................................................................................................................................................................................................................................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................CTACGx----GATCGGGTGGCGG........................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................................................AGG----GATCGGGTGGCGG........................................................................................................................................................................................................................................................................................................	16	2	0.50	0.00	0.00	0.00	0.50	0.00
.....................................................................................................................................................................................AGT----GATCGGGTGGCGG........................................................................................................................................................................................................................................................................................................	16	3	0.33	0.00	0.00	0.00	0.33	0.00

droEre2

CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTATC----GATCGGGTGGCGGATATACCCGTGCACAGATTGTAGCACACCCTATCGAATT---------G------------GAAT----TCCC-CATTAA----AA------------------------------------------------------------------------------------CT--------GA-GTGG------GCTTATATCGGCCGC---CCGATT-C----------------ACATACAACGACACAATAG--------------------------------CAGGATATAG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..................................................................................................................................................................T-------A---GCAACTTATC----GATCGGGTGGC..........................................................................................................................................................................................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................TATC----GATCGGGTGGCGGAT......................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................................TT---------G------------GAAT----TxCC-CATTAA----AA------------------------------------------------------------------------------------GT--------G...................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................................................................AACTTATC----GATCGGGTGGCG.........................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00

droEug1

CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTATC----GATCGGGTGGCGGAAAT----------AGATTGTAGGAAGTTTTACT-AATT---------G------------GACTTT--TCCC-TATATA-----A------------------------------------------------------------------------------------GT--------AA-ATAGAAAATAGTTTATTTTGGCTGC---CCGATT-T---------------AACATACAACGACACAATAG--------------------------------CAGGATATAG

Size

Hit Count

Total Norm

droBia1

CCGG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT------------------ATC----GATCGGGTGGCGGAAAT----------AGATTGTAGCC----------ATTT---------G------------GATT----TCCC-C--A-TAGAGAA------------------------------------------------------------------------------------GT--------GA-AT-------AGTTTATTTTGGCTGC---CCGATTCT---------------CACATACAACGACACAATAG--------------------------------CAGGATATAG

Size

Hit Count

Total Norm

droTak1

CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GTCACTTATCGATCGATCGGGTGGCGGAAAT----------AGATTGTAGAAAGCTCTATT-AATT---------GAAAAT-----------CCAATCCC-CATATA-----A------------------------------------------------------------------------------------GT--------AA-AT-------AGTTTATTTTGGCTGC---CCGATT-C---------------CACATACAACGACACAATAG--------------------------------CAGGATATAG

Size

Hit Count

Total Norm

droEle1

CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACACAGACGGACA-------A---GCAACTTATC----GATCGGGTGGCGGCAAT----------AGATTGTAGTAAGCTCTGTT-AATT---------G------------GATATTG--CCCCT--ATA-----A------------------------------------------------------------------------------------GTACAT----AAA-TA--TGATAGTTTATTTTGGCTGC---CCGATT-T----------------TAATACAACGACACAATAG--------------------------------CAGAATATAG

Size

Hit Count

Total Norm

droRho1

CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTATC----GATCGGGTAGCGGAATT----------AGATTGTAGTAAGCTCTATT-GATT---------G------------GATATTG--TCG-C--ATA-----A------------------------------------------------------------------------------------GTACGT----AA-AT-------AGTTCATTTTGGCTGC---CCGATT-C----------------ACATACAACGACACAATAG--------------------------------CAGGATATAG

Size

Hit Count

Total Norm

droFic1

CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCGGACGGACT-------G---GGAACTTATC----GATCTTATCG-----AT----------AACTTAT-----------------CGGTTAACT-TCGTTT-----------TCA--GCC-C--A-A-----A------------------------------------------------------------------------------------GT--------AAA-TA--TAGTAGTTTATTTTGGCTACCACCCGATT-C----------------ACATACAACGACACAATAG--------------------------------CAGGATATAG

Size

Hit Count

Total Norm

droKik1

ATTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---------------AAAAAATATATAAGGCATAG--------------------------------TATGGTATAG

Size

Hit Count

Total Norm

droAna3

CACT-----GCGATCTCGAGTACTTTGATCTC-------------------------------------------------------------------------------------------------------------------------------------------------TCTTCTC----A--GGGCCCCAAAAAGT----------ATGCTATGAAATATTTCGTT-TGCT---------A------------------------------------------------------------------------------------------------------------------AAG----TG--------TTTCAAG------GATTCTTTTGCGAGC---C----------------------------CACCTCAAGGATGT--------------------------------CAAACTCTAG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
......................................................................................................................................................................................................AAAAAGA----------ATTCTATGAAAT..............................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................................CTTTTC----A--GGGCCACAAAAA......................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...........GATCTCGAGGACTTTGAGC...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...................................................................................................................................................................................................................................ATTTCGTT-TGCT---------A------------------------------------------------------------------------------------------------------------------AAG----TG--------TTTCAAT------G......................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................................TTTAATT-TGCT---------A------------------------------------------------------------------------------------------------------------------AAG----TG--------T...................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droBip1

AAAAACACTGCGATCTCGAGTACTTTGATCTCTCTTCTCAGGGCCCCAAAAAGTATGCTATGAAATGTTTCATTGCCAAAGTGTTTCAGAGGATCCTTTTGAGAGCCCAACTCACGGACGTCAAACTCTAGAGATGTCTCTTTTAAACCGACTCAGACGGACTTTGGTCT--TTGCAGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA--AGG----CAGATCAGGCAGG---ACTATA-T----------------ACATACAACGACACAATAGCAGGACTAT---------------------------CTATAG

Size

Hit Count

Total Norm

dp4

C-AG--------------------------------------------------------------------------------------------------------------------------------------------------ACTTAGACGGACTTCAATCTA---GCAGTTTAAC----GATCGGGAAACGGGAAT----------AAACCAAAGTCGGC---------------------------------------------------------------------AGCCTATCCATCAAAATTCCAATATAATCACAACAGAAATCCAATTTGTTGC-----------------------------------T-------GGTTTATTTACGTTTC---TCGAGC-C----------------ACATACAACGACACAACAGCAGGTCTTCAGATAACTCATATGAAATAT---ACTTATGCGG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.............................................................................................................................................................................................AACGGGTAACGGGAAT----------AA........................................................................................................................................................................................................................................................................................	18	1	16.00	16.00	0.00	0.00	0.00
.....................................................................................................................................................................AATCTA---GCAGTTTAAC----GCTCGGGG.............................................................................................................................................................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00

droPer1

GCAT--------------------------------------------------------------------------------------------------------------------------------------------------ACATAGGCATCGC-------A---TCCA------------TCGGG--------------------------------------------------------------------GTC----ACCC-G--G-TGGAGGA---------------------------------------------------TAAATTTTGCGG--TGGTAACCCCGCAACACAAGCACTC------------------------------------------A---------------CACACACAGCGACCCAAACA----------------------------C---GTGCAATAAC

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TCAG--------------------------------------------------------------------------------------------------------------------------------------------------GCCTAAAATTAGT-------TGCCATAACT-CTC----ATTTATATAGTAGATTT----------GATGCTTTTTTG-----------------------------------------------------------------TTTT----------------------------------------------------TT--------T-----AAT----AT--------AT-TAAA------ATTTTTATTA-ATGC--------------ATTTCAGTGTAAAAATTAAAATGACACATTTT----------------------------T---CCTTACGTAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
....................................................................................................................................................................................................................................................................................................TTTC----------------------------------------------------TT--------T-----ATT----AT--------AT-TAAA------.......................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................................TTG-----------------------------------------------------------------TTTA----------------------------------------------------TT--------T-----AAA----AT--------AT-TA...............................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................................TTG-----------------------------------------------------------------TTTA----------------------------------------------------TT--------T-----AAA----AT--------AT-T................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................ATGC--------------AATTCAGTGTAAAACT..........................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................................................ATTCTTTTTTG-----------------------------------------------------------------TTTT----------------------------------------------------GT--------T-----.....................................................................................................................................	18	14	0.07	0.00	0.07	0.00	0.00
....................................................................................................................................................................................................................................................................................................TTTT----------------------------------------------------TG--------T-----AAA----AT--------AT-TAAA------A......................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................................T----AT--------AT-TGAA------ATGTTTATT..............................................................................................	18	4	0.25	0.00	0.25	0.00	0.00

droVir3

CAGG-----------------------------------------------------------------------------------------------------------------------------------------------------CAGACGAAA--------------GTATCTCC----GACCCCATGAAGTGTAT----------ATATTCT-----------------TGATCAGCATCAATAGCTGAGTCGAT-------------GTA-----GCCATGTCCGTCT------------------------------------------------------------------------------------------------GCCTGTCCGTCCGT---CCGTCC-GTATGTA--------------TGAACGCAAGGATCT--------------------------------CAGAACCTTT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................AACGCAAGGATCT--------------------------------CAGAACCT..	21	5	2.20	0.00	0.00	0.00	1.40	0.80
.........................................................................................................................................................................................................................................................................................................................................................................................................................................A--------------TGAACGCAAGGATCT--------------------------------CAGAACCT..	24	5	0.80	0.00	0.00	0.00	0.80	0.00
.................................................................................................................................................................................................................................................................GAGTCGAT-------------CTA-----GCCATGTCCGTCT------------------------------------------------------------------------------------------------......................................................................................................	24	8	0.50	0.50	0.00	0.00	0.00	0.00
.......................................................................................................................................................................................................................................................................................TA-----GCCATGTCCGTCT------------------------------------------------------------------------------------------------ATCTGTC...............................................................................................	22	11	0.36	0.00	0.00	0.00	0.00	0.36
............................................................................................................................................................................................................T----------ATATTCT-----------------TGATCAGCATCAATAGCC................................................................................................................................................................................................................................................	26	12	0.33	0.33	0.00	0.00	0.00	0.00
....................................................................................................................................................................................................................................................................TCGAT-------------CTA-----GCCATGTCCGTCT------------------------------------------------------------------------------------------------......................................................................................................	21	14	0.29	0.07	0.14	0.00	0.07	0.00
.........................................................................................................................................................................................................................................................................................................................................................................................................................................................GAACGCAAGGATCT--------------------------------AAGAGCC...	21	1	3.00	0.00	0.00	0.00	2.00	1.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................TATGTA--------------TGAACGCAAGGATCT--------------------------------GAGA......	25	6	0.50	0.00	0.00	0.00	0.50	0.00
.......................................................................................................................................................................................................................................................................................TA-----GCCATGTCCGTCT------------------------------------------------------------------------------------------------ATCTGT................................................................................................	21	14	0.21	0.00	0.07	0.00	0.00	0.14
............................................................................................................................................................................................................................................................................................................................................................................................................................................................CGCAAGGATCT--------------------------------CAGAACCT..	19	6	0.50	0.00	0.00	0.00	0.33	0.17
........................................................................................................................................................................................................................................................................................................................................................................................................................................................TGAACGCAAGGATCT--------------------------------CAGAACCT..	23	5	0.60	0.00	0.00	0.00	0.60	0.00
.....................................................................................................................................................................................................................................................................CGAT-------------CTA-----GCCATGTCCGTCT------------------------------------------------------------------------------------------------G.....................................................................................................	21	14	0.21	0.21	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................TCT-----------------TGATCAGCACCAATAGCCGAGTC...........................................................................................................................................................................................................................................	26	6	0.50	0.17	0.00	0.00	0.33	0.00
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................AACGCAAGGATCT--------------------------------CAGAGCCT..	21	6	0.50	0.00	0.00	0.00	0.00	0.50
....................................................................................................................................................................................................................................................................................................................................................................................................................................TATGTA--------------TGAACGCAAGGATCT--------------------------------CAGAACC...	28	5	0.60	0.00	0.00	0.00	0.60	0.00

droMoj3

GTAG--------------------------------------------------------------------------------------------------------------------------------------------------ATTCAGTTGTACT-------TTATAGAA--TTTC----GATTTA------------------------------------------TGT----------TAAAAT-----------TCA--TCC-C--T-T-------------------------------------------------------------------AC--------C-----AAT----AT--------AT-ATG-------TGTTTTTTCAAATGC-ATGCATT--T---------------TAATGGTATCAACACAATTT----------------------------G---AAAGTCTCAT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.TAG--------------------------------------------------------------------------------------------------------------------------------------------------ATTCAGTAGTACT-------TA.....................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................ACGTACT-------TTATAGAA--TTTC----GATTT................................................................................................................................................................................................................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................ATGTACT-------TTATGGAA--TTTC----GATT.................................................................................................................................................................................................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00

droGri2

CTGA--------------------------------------------------------------------------------------------------------------------------------------------------ACATAACTGAATA-------A---ATT-----------------------------------------------------------------------------------------------------------------------------------------------------CACAACAT--ATTTAGTCAGTTACTTATGTATATACTTGATACAATTGTGCAAACATGCAAA------ATTCCAATTAAATGT--------------------------------------CACAATAT------------------ATAAAAACTGATGCGAGAAGATTG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:22:10 EDT

dme-mir-4940

chr3L:9137692-9137797 +

Known_mirbase

three_prime_UTR

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup